uk.ac.sanger.psu.gfmerge.analysis.tools
Class HighScoringPath

java.lang.Object
  extended by uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath

public class HighScoringPath
extends java.lang.Object


Constructor Summary
HighScoringPath()
           
 
Method Summary
private static java.util.HashMap calcHighScoringPath(java.util.HashMap clusteredObjScoreHash, boolean isAverage)
           
private static java.util.TreeMap getAllPaths(java.util.TreeMap allPathList, java.util.ArrayList singlePathArr, java.util.HashMap objScoreHash, boolean isAverage)
           
static java.util.HashMap getHighScoringPath(java.util.HashMap nonClusteredObjScoreHash, java.util.ArrayList arrListOfGmRegions, boolean isAverage)
           
private static java.util.ArrayList getNonOverlappingObjs(java.util.ArrayList singlePathArr, java.util.HashMap objScoreHash)
           
private static double getPathScore(java.util.ArrayList pathArr, java.util.HashMap objScoreHash, boolean isAverage)
           
private static boolean isNonOverlappingDownstreamObjFurtherUpstream(java.util.ArrayList singlePathArr)
           
private static boolean isNonOverlappingObjUpstream(java.util.ArrayList singlePathArr, java.util.ArrayList arrOfNonOverlappingObjs)
           
static java.util.ArrayList removeLowScoreGmsFromRegArr(java.util.ArrayList _arrListOfGMRegions, java.util.HashMap highScorePathGms)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

HighScoringPath

public HighScoringPath()
Method Detail

getHighScoringPath

public static java.util.HashMap getHighScoringPath(java.util.HashMap nonClusteredObjScoreHash,
                                                   java.util.ArrayList arrListOfGmRegions,
                                                   boolean isAverage)

calcHighScoringPath

private static java.util.HashMap calcHighScoringPath(java.util.HashMap clusteredObjScoreHash,
                                                     boolean isAverage)

getAllPaths

private static java.util.TreeMap getAllPaths(java.util.TreeMap allPathList,
                                             java.util.ArrayList singlePathArr,
                                             java.util.HashMap objScoreHash,
                                             boolean isAverage)

getPathScore

private static double getPathScore(java.util.ArrayList pathArr,
                                   java.util.HashMap objScoreHash,
                                   boolean isAverage)

getNonOverlappingObjs

private static java.util.ArrayList getNonOverlappingObjs(java.util.ArrayList singlePathArr,
                                                         java.util.HashMap objScoreHash)

isNonOverlappingObjUpstream

private static boolean isNonOverlappingObjUpstream(java.util.ArrayList singlePathArr,
                                                   java.util.ArrayList arrOfNonOverlappingObjs)

isNonOverlappingDownstreamObjFurtherUpstream

private static boolean isNonOverlappingDownstreamObjFurtherUpstream(java.util.ArrayList singlePathArr)

removeLowScoreGmsFromRegArr

public static java.util.ArrayList removeLowScoreGmsFromRegArr(java.util.ArrayList _arrListOfGMRegions,
                                                              java.util.HashMap highScorePathGms)